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config.yaml
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data_files:
- "B2_samples.csv"
project_prefix:
'/mnt/storage1/projects/research'
fasta_filename_template:
'Sample_{sample}/{sample}_consensus.fa'
filename_gisaid_metadata:
"{batch}_gisaid_meta.csv"
filename_nextstrain_metadata:
"{batch}_nextstrain_meta.tsv"
gisaid_metadata:
submitter: "[email protected]"
fn: "hCov19_UKT_{batch}.fasta"
covv_virus_name: "hCov-19/Germany/BW-UKT-{sample}/{year}"
covv_type: "betacoronavirus"
covv_passage: "Original"
covv_collection_date: "{year}-{month}-{day}"
covv_location: "Europe/Germany/Baden-Württemberg"
covv_add_location:
covv_host: "Human"
covv_add_host_info:
covv_gender: "unknown"
covv_patient_age: "unknown"
covv_patient_status: "unknown"
covv_specimen:
covv_outbreak:
covv_last_vaccinated:
covv_treatment:
covv_seq_technology: "Illumina NextSeq Twist"
covv_assembly_method:
covv_coverage:
covv_orig_lab: "Institute of Medical Genetics and Applied Genomics"
covv_orig_lab_addr: "Calwerstr. 7 72076 Tübingen"
covv_provider_sample_id:
covv_subm_lab: "Institute of Medical Genetics and Applied Genomics"
covv_subm_lab_addr: "Calwerstr. 7 72076 Tübingen"
covv_subm_sample_id:
covv_authors: "\\\"Caspar Gross, Tina Ganzenmüller, Siri Göpel, Michaela Pogoda, Daniela Bezdan, Michael Sonnabend, Angel Angelov, Nicolas Casadei, Stephan Ossowski, Thomas Iftner, Michael Bitzer \\\""
nextstrain_metadata:
strain: "hCov-19/Germany/BW-UKT-{sample}/{year}"
virus: "ncov"
gisaid_epi_isl:
genbank_accession:
date: "{year}-{month}-{day}"
region: "Europe"
country: "Germany"
division: "Baden-Württemberg"
location:
region_exposure:
country_exposure:
division_exposure:
segment:
length:
host: "human"
age: "unknown"
sex: "unknown"
originating_lab: "Institute of Medical Genetics and Applied Genomics, Calwerstr. 7 72076 Tübingen"
submitting_lab: "Institute of Medical Genetics and Applied Genomics, Calwerstr. 7 72076 Tübingen"
authors: "\\\"Caspar Gross, Tina Ganzenmüller, Siri Göpel, Michaela Pogoda, Daniela Bezdan, Michael Sonnabend, Angel Angelov, Nicolas Casadei, Stephan Ossowski, Thomas Iftner, Michael Bitzer \\\""
url:
title:
date_submitted: "{today}"
samples: # list of samples without the prefix "Sample_". If empty: Uses all folders with Sample_ prefix
#samples: 21014a008
target_twist: '/mnt/storage2/users/ahcepev1/pipelines/COVID-19/twist_sars_cov2.bed' # e.g: /root/[PROJECT_NAME]/twist_sars_cov2.bed
reference: '/mnt/storage2/users/ahcepev1/pipelines/COVID-19/ref/MN908947.3.fasta' # e.g: /root/[PROJECT_NAME]/ref/MN908947.3.fasta
adapter1: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' # Adapter read 1
adapter2: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' # Adapter read 2
krakendb: '/mnt/storage2/users/ahcepev1/pipelines/COVID-19/kraken2_human' # extracted kraken path
#umiVar: 'python3 /mnt/users/ahgrosc1/dev/umivar2'
#umiVar: 'python3 /mnt/storage2/users/ahgrosc1/dev/umivar2' #umivar directory
umiVar: 'python3 /mnt/storage2/users/ahcepev1/tools/umiVar2-2023_06/umiVar.py'
threads: 8 # number of threads
umivar:
ac: "3"
ns: "-1"
sb: "0"